Say youve got a problem. Maybe you cant figure out how to make a gene therapy vector that cant be detected by pre-existing antibodies that everybody already has. Maybe you are trying to figure out how to make an effective HIV-1 vaccine.

You could figure out which portions of AAV or HIV-1 are really important, try to make point mutations here and there, trying to get the virus to do what you want it to do… Or you could just let evolution do all the hard work for you– Letting random mutation and natural selection identify a variant that can perform the tricks youre after.

A lab has already done that with AAV. They started with ‘diversity’ and used evolution to identify gene therapy vectors that could target brains, livers, lungs, etc, and CANT be recognized by pre-existing antibodies.

Now another lab has caught onto this cool idea to help make better HIV-1 vaccines!

This lab is starting from a different angle. Instead of starting with diversity and having evolution narrow possibilities down to one/a few variants, this lab is starting with one variant, and letting random mutation and natural selection generate lots of different solutions!

So here is the problem– We cant figure out how to make a vaccine against HIV-1 that generates lots of ‘broadly neutralizing antibodies’, antibodies that can still recognize viruses if they mutate away from what was put into the vaccine.

We can make slightly better vaccines if we chop up env a little bit. If we cut out two really variable regions of env, the Variable 1 loop and the Variable 2 loop, we can make higher affinity antibodies to neutralize viruses, because your immune system can focus on a REALLY important region of env, the Variable 3 loop.

It would also be really cool if we could make envelope trimers that can be excreted by cell lines, so we could just throw them into a vaccine instead of dummy viruses. It would be a LOT easier to make huge quantities of secreted protein, rather than purifying delicate dummy viruses… but if you chop out V1/V2, the secretable Env trimers we have just dont work.

SO! This lab created a whole bunch of potential V1/V2 deletion variants by deleting this region in a few different ways. All of these variants just didnt work as well as a nice wild-type envelope protein. So they took a population of each variant and repeatedly passaged them in T-cells for four and a half months (!!!). Their logic was that even though their V1/V2 deleted viruses were ‘crippled’, the populations would accumulate compensatory secondary mutations to regain their replicative capacity. We know HIV-1 can do this, because thats exactly what happens with HIV-1 drug resistance– Initial mutations to escape antiretrovirals come at a fitness cost, but over time, compensatory mutations lead to a virus that is super fit AND can escape the antiretrovirals. So why not use HIV-1s evolutionary abilities to generate a weapon we can use against it!

At the end of 4 1/2 months, some of the populations konked out. The viruses were crappy at replicating, and eventually went extinct. But some populations got better at replicating, AND more stable… which means they are not only better for making antibodies, they are also better for generating those secreted envelope trimers for vaccines!

Now, this doesnt mean that we will have an HIV-1 vaccine in 2 months.

It doesnt mean that any of the clinical research that comes out of this particular study will eventually end up in a vaccine.

But, its a new tool. Its a new weapon we can at least try against HIV-1.

There’s also genetic algorithms, in which we use natural selection to find answers to engineering, mathematical and even biology problems (and make a mockery of Dembski’s arguments for ID while at it). I’m doing an honour’s year in it.

Regarding [#6], you’re confused if you think an algorithm you’ve intelligently designed is somehow making a mockery of Dembski.

WW, you’re a fool. Dembski persistently misrepresents GAs in order to avoid the fact that they generate “CSI” in exactly the same sense WAD uses the term in No Free Lunch. WW is in essence saying that if an intelligently designed experiment that uses solely Darwinian evolutionary mechanisms in an intelligently designed Petri dish produces, say, a novel metabolic process, that process was intelligently designed. Hell, on WW’s bizarre view, that one can design an algorithm to model hurricane dynamics means that hurricanes are intelligently designed.

Why don’t you just isolate the proteins HIV binds to when entering a cell, find the genes that code for the protein(s) or reverse engineer a gene from the protein, implant the gene into e. coli and let the bacteria replicate the protein, then use that protein to trigger a “premature ejaculation” of the viruses before they can infect cells? Or I just missing some crucial information as to why that’s impossible/ineffective?

Lance, even using Creationists IDiotic definition of ‘macroevolution’, these studies most certainly DO result in macroevolution. The AAV study would be comparable to smashing the genome of Balaenoptera acutorostrata, bonaerensis, borealis, brydei, edeni, omurai, musculus, and physalus and getting a brand new species of whale, Balaenoptera brandnewicus.

How, exactly, is fragmenting the genome of eight species of virus to recombine them to make numerous brand new species of virus not macroevolution

As a layman, and you can correct me if I am wrong, but first, it sounds like the splicing is a form of intelligent design.

Second, in the context of the tree of life, even assuming for the sake of argument that you’re correct in characterizing genetically distinct populations of viruses as “species” (and I am certainly not qualified to argue otherwise), in the context of the big picture–the diversity of life, e.g., using the tree of life, are you forming new trunks, or relatively infinitesimal branches?

WW: “You can’t have macroevolution with new species”
ERV: “This *is* a new species.”
WW: “But you can’t have macroevolution with new genera…”
Never let creationists enter a football field – they would move the goalposts faster than you can shoot at them…

Why don’t you just isolate the proteins HIV binds to when entering a cell, find the genes that code for the protein(s) or reverse engineer a gene from the protein, implant the gene into e. coli and let the bacteria replicate the protein, then use that protein to trigger a “premature ejaculation” of the viruses before they can infect cells?

Well the problem is that there’s a lot of sugars on that envelop protein. E coli can’t really make sugars on proteins so it really messes up the protein and doesn’t look like the real thing any more. So you have to vaccinate with the protein produced by mammalian cells. And then still you have the problem that most of the antibodies will be directed against the V1 and V2. Therefore this group is trying to take them out.

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